Multiple sequence alignment - TraesCS4A01G294500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G294500 chr4A 100.000 4346 0 0 1 4346 595843117 595847462 0.000000e+00 8026
1 TraesCS4A01G294500 chr4B 92.597 3215 158 46 1203 4346 13974135 13977340 0.000000e+00 4545
2 TraesCS4A01G294500 chr4B 82.629 639 55 18 128 759 13973118 13973707 8.330000e-142 514
3 TraesCS4A01G294500 chr4B 90.698 301 19 4 879 1171 13973741 13974040 4.070000e-105 392
4 TraesCS4A01G294500 chr4B 89.216 102 6 3 1 102 13972954 13973050 5.900000e-24 122
5 TraesCS4A01G294500 chr4D 93.217 2226 106 27 2144 4346 7759878 7757675 0.000000e+00 3232
6 TraesCS4A01G294500 chr4D 85.305 1048 67 41 128 1171 7761952 7760988 0.000000e+00 1002
7 TraesCS4A01G294500 chr4D 96.203 395 14 1 1749 2143 7760359 7759966 0.000000e+00 645
8 TraesCS4A01G294500 chr4D 82.646 582 42 26 1183 1723 7760919 7760356 1.100000e-125 460
9 TraesCS4A01G294500 chr4D 90.385 104 4 3 1 104 7762118 7762021 9.810000e-27 132


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G294500 chr4A 595843117 595847462 4345 False 8026.00 8026 100.0000 1 4346 1 chr4A.!!$F1 4345
1 TraesCS4A01G294500 chr4B 13972954 13977340 4386 False 1393.25 4545 88.7850 1 4346 4 chr4B.!!$F1 4345
2 TraesCS4A01G294500 chr4D 7757675 7762118 4443 True 1094.20 3232 89.5512 1 4346 5 chr4D.!!$R1 4345

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
335 389 0.035458 CGTTTCTTGGCTCCTGTCCT 59.965 55.0 0.0 0.0 0.0 3.85 F
350 404 0.609406 GTCCTGGCCCTTTCTTGGTC 60.609 60.0 0.0 0.0 0.0 4.02 F
1219 1373 0.178975 TGTTTACACCAGCCCCAAGG 60.179 55.0 0.0 0.0 0.0 3.61 F
1710 1937 0.102300 GCGCCAACCACTTTTGACTT 59.898 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 1337 0.854218 TTCCTTGGGGCTGGTGTAAA 59.146 50.0 0.00 0.0 0.00 2.01 R
1689 1916 0.948678 GTCAAAAGTGGTTGGCGCTA 59.051 50.0 7.64 0.0 0.00 4.26 R
2729 3048 0.885879 TAGGCGCTCGACTTCTTCAA 59.114 50.0 7.64 0.0 34.01 2.69 R
3378 3700 0.035439 CGGCAGGAACACCCAGTTAT 60.035 55.0 0.00 0.0 41.51 1.89 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.746904 TCAGTATTCAATGCGGTGGTTG 59.253 45.455 0.00 0.00 0.00 3.77
36 37 0.249238 TTCAATGCGGTGGTTGCAAC 60.249 50.000 21.59 21.59 46.87 4.17
39 40 1.106351 AATGCGGTGGTTGCAACTGA 61.106 50.000 27.64 13.05 46.87 3.41
43 44 1.827789 GGTGGTTGCAACTGAGGCA 60.828 57.895 27.64 14.67 40.00 4.75
64 65 4.843331 AGGGGCGGATGGATGGGT 62.843 66.667 0.00 0.00 0.00 4.51
65 66 4.586235 GGGGCGGATGGATGGGTG 62.586 72.222 0.00 0.00 0.00 4.61
66 67 4.586235 GGGCGGATGGATGGGTGG 62.586 72.222 0.00 0.00 0.00 4.61
67 68 3.488569 GGCGGATGGATGGGTGGA 61.489 66.667 0.00 0.00 0.00 4.02
104 109 5.860716 GCTTTTCCTTCTTCAAGCAACATAG 59.139 40.000 0.00 0.00 41.16 2.23
105 110 5.964958 TTTCCTTCTTCAAGCAACATAGG 57.035 39.130 0.00 0.00 0.00 2.57
106 111 4.908601 TCCTTCTTCAAGCAACATAGGA 57.091 40.909 0.00 0.00 0.00 2.94
107 112 4.836825 TCCTTCTTCAAGCAACATAGGAG 58.163 43.478 0.00 0.00 0.00 3.69
109 114 5.483937 TCCTTCTTCAAGCAACATAGGAGTA 59.516 40.000 0.00 0.00 0.00 2.59
110 115 5.814705 CCTTCTTCAAGCAACATAGGAGTAG 59.185 44.000 0.00 0.00 0.00 2.57
113 118 5.717178 TCTTCAAGCAACATAGGAGTAGTCT 59.283 40.000 0.00 0.00 0.00 3.24
114 119 6.211584 TCTTCAAGCAACATAGGAGTAGTCTT 59.788 38.462 0.00 0.00 0.00 3.01
126 161 1.099689 GTAGTCTTCGCTCTGCTCCT 58.900 55.000 0.00 0.00 0.00 3.69
129 164 1.000270 TCTTCGCTCTGCTCCTCCT 60.000 57.895 0.00 0.00 0.00 3.69
133 180 2.489275 CGCTCTGCTCCTCCTCTCC 61.489 68.421 0.00 0.00 0.00 3.71
137 184 3.284251 TGCTCCTCCTCTCCCCCA 61.284 66.667 0.00 0.00 0.00 4.96
139 186 2.041405 CTCCTCCTCTCCCCCACC 60.041 72.222 0.00 0.00 0.00 4.61
140 187 2.874245 TCCTCCTCTCCCCCACCA 60.874 66.667 0.00 0.00 0.00 4.17
141 188 2.366167 CCTCCTCTCCCCCACCAG 60.366 72.222 0.00 0.00 0.00 4.00
143 190 3.615811 TCCTCTCCCCCACCAGCT 61.616 66.667 0.00 0.00 0.00 4.24
211 265 2.202570 GCAGCAAGCAATGGAGCG 60.203 61.111 0.00 0.00 44.79 5.03
213 267 2.042259 CAGCAAGCAATGGAGCGGA 61.042 57.895 0.00 0.00 40.15 5.54
265 319 0.759812 GTGTAGTAGGGCTCCCTCCC 60.760 65.000 11.41 3.65 44.43 4.30
272 326 4.890306 GGCTCCCTCCCTCCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
332 386 1.339151 GGATCGTTTCTTGGCTCCTGT 60.339 52.381 0.00 0.00 0.00 4.00
335 389 0.035458 CGTTTCTTGGCTCCTGTCCT 59.965 55.000 0.00 0.00 0.00 3.85
349 403 1.360393 TGTCCTGGCCCTTTCTTGGT 61.360 55.000 0.00 0.00 0.00 3.67
350 404 0.609406 GTCCTGGCCCTTTCTTGGTC 60.609 60.000 0.00 0.00 0.00 4.02
460 518 4.773117 GCTGCTGCTGCTTTCGGC 62.773 66.667 22.10 9.14 44.80 5.54
487 545 2.620585 GGTTTCTTGCTCTTGCTCTTGT 59.379 45.455 0.00 0.00 40.48 3.16
493 551 2.224606 TGCTCTTGCTCTTGTTCTTGG 58.775 47.619 0.00 0.00 40.48 3.61
494 552 1.538950 GCTCTTGCTCTTGTTCTTGGG 59.461 52.381 0.00 0.00 36.03 4.12
498 561 1.228552 GCTCTTGTTCTTGGGGGCA 60.229 57.895 0.00 0.00 0.00 5.36
531 594 3.375642 GTGGAGCTTCTGTTTGCTTTTC 58.624 45.455 0.00 0.00 39.91 2.29
532 595 2.362077 TGGAGCTTCTGTTTGCTTTTCC 59.638 45.455 0.00 0.00 39.91 3.13
555 618 1.176527 CCTTTGATTGATGGTGCGGT 58.823 50.000 0.00 0.00 0.00 5.68
557 620 1.541147 CTTTGATTGATGGTGCGGTGT 59.459 47.619 0.00 0.00 0.00 4.16
583 646 1.102222 TTTTGGCCGTTTGGTAGCGT 61.102 50.000 0.00 0.00 37.67 5.07
636 699 4.609018 AATGGAGATCCGCCCGCG 62.609 66.667 0.00 0.00 39.43 6.46
692 755 2.575525 CGCTCGCTCACAGAGTCG 60.576 66.667 0.00 0.00 37.99 4.18
755 818 2.653448 CAGGAGCGCGTCTGATCG 60.653 66.667 22.54 1.45 33.11 3.69
765 828 1.227973 GTCTGATCGGATTGGGGCC 60.228 63.158 7.68 0.00 0.00 5.80
768 831 2.403132 CTGATCGGATTGGGGCCTCC 62.403 65.000 0.00 0.72 0.00 4.30
809 872 1.526917 GGAGACGCCAATGGGGATG 60.527 63.158 23.60 0.00 40.01 3.51
818 881 2.800250 CCAATGGGGATGGATAGCTTC 58.200 52.381 0.00 0.00 40.56 3.86
819 882 2.430465 CAATGGGGATGGATAGCTTCG 58.570 52.381 0.00 0.00 0.00 3.79
823 886 2.375766 GGATGGATAGCTTCGCGCG 61.376 63.158 26.76 26.76 45.59 6.86
824 887 1.371758 GATGGATAGCTTCGCGCGA 60.372 57.895 31.40 31.40 45.59 5.87
848 911 1.068588 TCATCATAGCAGGCCGTGTAC 59.931 52.381 0.00 0.00 0.00 2.90
854 917 1.101331 AGCAGGCCGTGTACTAGTAC 58.899 55.000 23.58 23.58 36.63 2.73
858 921 2.290093 CAGGCCGTGTACTAGTACTAGC 59.710 54.545 28.56 25.51 36.66 3.42
861 924 2.286891 GCCGTGTACTAGTACTAGCAGC 60.287 54.545 28.56 20.47 36.66 5.25
875 951 4.081030 CAGCAGCGCGTGTTGGAG 62.081 66.667 14.80 0.00 33.85 3.86
937 1013 6.128172 GGATGTTGTTCTCTGAATGAACGAAT 60.128 38.462 0.00 0.00 44.67 3.34
963 1042 1.998315 CAGGTTCATCTTCTCAGCGTG 59.002 52.381 0.00 0.00 0.00 5.34
977 1062 0.870307 AGCGTGTGTTCTGTGACGAC 60.870 55.000 0.00 0.00 33.64 4.34
1153 1238 3.253432 CCTTGTGGTTTCCAAGTTAGAGC 59.747 47.826 0.00 0.00 38.07 4.09
1186 1317 5.408880 TGTAACCATGAGAACATCGGTTA 57.591 39.130 0.00 0.94 42.21 2.85
1187 1318 5.984725 TGTAACCATGAGAACATCGGTTAT 58.015 37.500 17.69 0.00 43.26 1.89
1188 1319 7.114866 TGTAACCATGAGAACATCGGTTATA 57.885 36.000 17.69 14.85 43.26 0.98
1189 1320 6.982141 TGTAACCATGAGAACATCGGTTATAC 59.018 38.462 17.69 13.06 43.26 1.47
1190 1321 5.871396 ACCATGAGAACATCGGTTATACT 57.129 39.130 0.00 0.00 37.36 2.12
1191 1322 5.844004 ACCATGAGAACATCGGTTATACTC 58.156 41.667 0.00 0.00 37.36 2.59
1202 1337 5.401531 TCGGTTATACTCAAGAGCTTTGT 57.598 39.130 0.00 0.00 0.00 2.83
1211 1346 4.576463 ACTCAAGAGCTTTGTTTACACCAG 59.424 41.667 0.00 0.00 0.00 4.00
1215 1368 0.317160 GCTTTGTTTACACCAGCCCC 59.683 55.000 3.00 0.00 0.00 5.80
1217 1370 2.035632 CTTTGTTTACACCAGCCCCAA 58.964 47.619 0.00 0.00 0.00 4.12
1219 1373 0.178975 TGTTTACACCAGCCCCAAGG 60.179 55.000 0.00 0.00 0.00 3.61
1229 1383 2.094675 CAGCCCCAAGGAATAACACTG 58.905 52.381 0.00 0.00 33.47 3.66
1231 1385 1.005450 GCCCCAAGGAATAACACTGGA 59.995 52.381 0.00 0.00 33.47 3.86
1235 1389 2.615493 CCAAGGAATAACACTGGAGCGT 60.615 50.000 0.00 0.00 0.00 5.07
1248 1402 2.453521 TGGAGCGTCCAGTACTTATGT 58.546 47.619 0.00 0.00 42.67 2.29
1249 1403 3.623703 TGGAGCGTCCAGTACTTATGTA 58.376 45.455 0.00 0.00 42.67 2.29
1250 1404 4.212716 TGGAGCGTCCAGTACTTATGTAT 58.787 43.478 0.00 0.00 42.67 2.29
1251 1405 4.037565 TGGAGCGTCCAGTACTTATGTATG 59.962 45.833 0.00 0.00 42.67 2.39
1252 1406 4.547532 GAGCGTCCAGTACTTATGTATGG 58.452 47.826 0.00 0.00 33.05 2.74
1253 1407 3.958798 AGCGTCCAGTACTTATGTATGGT 59.041 43.478 0.00 0.00 33.30 3.55
1263 1417 9.293404 CAGTACTTATGTATGGTAGGCTAGTTA 57.707 37.037 0.00 0.00 0.00 2.24
1377 1534 7.086685 TCCTTTTTACAGAGGTCCAGTTAAT 57.913 36.000 0.00 0.00 34.57 1.40
1406 1571 9.556030 GCTGTTGAACATAGTACTAATTTTTCC 57.444 33.333 6.70 0.00 0.00 3.13
1411 1580 9.158233 TGAACATAGTACTAATTTTTCCCTTCG 57.842 33.333 6.70 0.00 0.00 3.79
1429 1598 5.178252 CCCTTCGCTACACATATTCTTGATG 59.822 44.000 0.00 0.00 0.00 3.07
1440 1609 9.740239 ACACATATTCTTGATGTTATTGCAATC 57.260 29.630 16.86 2.89 35.31 2.67
1492 1681 8.911662 CGAAAGTTTAAACACCATTAAATCCAG 58.088 33.333 20.06 0.00 37.17 3.86
1612 1825 7.461182 TCAACCATATTTTTCCATCTTCGTT 57.539 32.000 0.00 0.00 0.00 3.85
1626 1853 7.386851 TCCATCTTCGTTAATCTCAGAACTTT 58.613 34.615 0.00 0.00 0.00 2.66
1635 1862 9.329913 CGTTAATCTCAGAACTTTTAAATGTGG 57.670 33.333 7.44 2.11 0.00 4.17
1639 1866 4.854399 TCAGAACTTTTAAATGTGGCACG 58.146 39.130 13.77 0.00 0.00 5.34
1648 1875 7.923878 ACTTTTAAATGTGGCACGATTTACTTT 59.076 29.630 22.94 13.10 0.00 2.66
1656 1883 5.121768 GTGGCACGATTTACTTTACATCAGT 59.878 40.000 0.00 0.00 0.00 3.41
1660 1887 7.438459 GGCACGATTTACTTTACATCAGTATCT 59.562 37.037 0.00 0.00 0.00 1.98
1689 1916 6.708054 GGCTGCTGTCTATATCAATTTACACT 59.292 38.462 0.00 0.00 0.00 3.55
1694 1921 7.410942 GCTGTCTATATCAATTTACACTAGCGC 60.411 40.741 0.00 0.00 0.00 5.92
1709 1936 0.751643 AGCGCCAACCACTTTTGACT 60.752 50.000 2.29 0.00 0.00 3.41
1710 1937 0.102300 GCGCCAACCACTTTTGACTT 59.898 50.000 0.00 0.00 0.00 3.01
1719 1946 3.829601 ACCACTTTTGACTTCACAAACCA 59.170 39.130 0.00 0.00 39.08 3.67
1720 1947 4.082245 ACCACTTTTGACTTCACAAACCAG 60.082 41.667 0.00 0.00 39.08 4.00
1721 1948 4.082245 CCACTTTTGACTTCACAAACCAGT 60.082 41.667 0.00 0.00 39.08 4.00
1723 1950 5.572896 CACTTTTGACTTCACAAACCAGTTC 59.427 40.000 0.00 0.00 39.08 3.01
1724 1951 5.476945 ACTTTTGACTTCACAAACCAGTTCT 59.523 36.000 0.00 0.00 39.08 3.01
1726 1953 4.214986 TGACTTCACAAACCAGTTCTCA 57.785 40.909 0.00 0.00 0.00 3.27
1728 1955 5.192927 TGACTTCACAAACCAGTTCTCAAT 58.807 37.500 0.00 0.00 0.00 2.57
1732 1960 6.322201 ACTTCACAAACCAGTTCTCAATCATT 59.678 34.615 0.00 0.00 0.00 2.57
1736 1964 6.584942 CACAAACCAGTTCTCAATCATTCATG 59.415 38.462 0.00 0.00 0.00 3.07
1737 1965 6.491062 ACAAACCAGTTCTCAATCATTCATGA 59.509 34.615 0.00 0.00 41.70 3.07
1745 1973 9.132923 AGTTCTCAATCATTCATGAGCATATTT 57.867 29.630 0.00 0.00 42.21 1.40
1763 1991 8.270744 AGCATATTTCTAGTTTCTTCCTGTGAT 58.729 33.333 0.00 0.00 0.00 3.06
1769 1997 8.848474 TTCTAGTTTCTTCCTGTGATAAAAGG 57.152 34.615 0.00 0.00 34.65 3.11
1770 1998 5.966742 AGTTTCTTCCTGTGATAAAAGGC 57.033 39.130 0.00 0.00 33.25 4.35
1809 2037 3.006967 GGCTTATGACCTCACACGGATAT 59.993 47.826 0.00 0.00 0.00 1.63
1917 2145 6.495181 AGCTAGTACATATATGTTGCTCCAGT 59.505 38.462 22.90 9.65 41.97 4.00
1936 2164 7.699812 GCTCCAGTCATGATATTTTCTTTTCAC 59.300 37.037 0.00 0.00 0.00 3.18
1938 2166 8.733458 TCCAGTCATGATATTTTCTTTTCACAG 58.267 33.333 0.00 0.00 0.00 3.66
1964 2192 0.179043 TAGCGGCAAACTGACAACCA 60.179 50.000 1.45 0.00 0.00 3.67
2056 2284 6.705302 TGTTGCATCTACAGATCTTTTCTCT 58.295 36.000 0.00 0.00 31.21 3.10
2062 2290 5.826586 TCTACAGATCTTTTCTCTGATCGC 58.173 41.667 7.28 0.00 42.22 4.58
2200 2515 4.935702 TGGACTTTTGTTTCATTGCTCAG 58.064 39.130 0.00 0.00 0.00 3.35
2222 2537 0.535780 CACATGTGTGTCCTGGCTGT 60.536 55.000 18.03 0.00 40.96 4.40
2342 2657 9.066892 ACCAAATCTTACATATATGCAATTCGT 57.933 29.630 12.79 5.25 0.00 3.85
2454 2773 5.339008 TGTCAACGGTCTAGATATTTGCT 57.661 39.130 0.00 0.00 0.00 3.91
2462 2781 7.328737 ACGGTCTAGATATTTGCTAACTTGTT 58.671 34.615 0.00 0.00 0.00 2.83
2469 2788 8.165239 AGATATTTGCTAACTTGTTTGTGACA 57.835 30.769 0.00 0.00 36.19 3.58
2470 2789 8.629158 AGATATTTGCTAACTTGTTTGTGACAA 58.371 29.630 0.00 0.00 45.70 3.18
2497 2816 2.292016 TGCTTATGGTTGTGTGTTTCCG 59.708 45.455 0.00 0.00 0.00 4.30
2539 2858 3.347216 TCTTTCTCTGGTTGCAATAGCC 58.653 45.455 0.59 0.00 41.13 3.93
2575 2894 0.111639 GGGAGGGGCAGTTTTACACA 59.888 55.000 0.00 0.00 0.00 3.72
2702 3021 7.584847 GTGTTGATTGAAATGCATTGTTCTTTG 59.415 33.333 13.82 0.00 0.00 2.77
2729 3048 0.321653 GTTCCTTGACACCGCTGGAT 60.322 55.000 1.50 0.00 0.00 3.41
2960 3281 6.095440 AGTTGCATTGACAAAGTAACTTCACT 59.905 34.615 17.56 0.35 0.00 3.41
3008 3329 2.432444 TGCACTAGTATTTGGTGGTGC 58.568 47.619 8.63 8.63 46.65 5.01
3022 3343 3.383185 TGGTGGTGCGATCTTTTCTTTTT 59.617 39.130 0.00 0.00 0.00 1.94
3193 3514 4.218200 TGCCATCTGACACAATTTTACCTG 59.782 41.667 0.00 0.00 0.00 4.00
3358 3680 1.680207 GGTCGTAATCGGAGTAGGCTT 59.320 52.381 0.00 0.00 37.69 4.35
3378 3700 1.891919 GCGGACCAGAAGTGCAACA 60.892 57.895 0.00 0.00 41.43 3.33
3610 3932 2.289547 GGCTAAATCGCGCTATTTTCCA 59.710 45.455 22.81 6.68 31.63 3.53
3852 4179 3.809279 CCTGTTTCCTGGTCAAATTTTGC 59.191 43.478 4.19 0.39 0.00 3.68
3869 4197 5.818136 TTTTGCTATATTCGCTCTTTGCT 57.182 34.783 0.00 0.00 40.11 3.91
3870 4198 4.801147 TTGCTATATTCGCTCTTTGCTG 57.199 40.909 0.00 0.00 40.11 4.41
3913 4241 2.622942 TGCAAACCATCTCCAAACTGAC 59.377 45.455 0.00 0.00 0.00 3.51
3925 4254 3.396276 TCCAAACTGACCCCATCAACTAA 59.604 43.478 0.00 0.00 36.69 2.24
3986 4315 7.390823 TCTGTTGAATAACCTGTTGCATACTA 58.609 34.615 0.00 0.00 35.92 1.82
4016 4345 7.759489 ACATCAAACTTAGGAGCAACAATTA 57.241 32.000 0.00 0.00 0.00 1.40
4104 4455 5.714333 AGTATGGGCATTTACATGACAAACA 59.286 36.000 0.00 0.00 40.81 2.83
4129 4480 5.890424 TGAACGAAAAAGAAAAGACAGGT 57.110 34.783 0.00 0.00 0.00 4.00
4146 4497 3.383681 TGGGCACGGTAGCGCTTA 61.384 61.111 18.68 0.00 46.41 3.09
4154 4505 3.043586 CACGGTAGCGCTTAAGAGTATG 58.956 50.000 18.68 0.00 0.00 2.39
4172 4523 3.834489 ATGTCAGATAAGGCACAGGAG 57.166 47.619 0.00 0.00 0.00 3.69
4245 4598 3.924073 CAGACGACGAATGTGACCAAATA 59.076 43.478 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.033920 CCCCTTTTTGCCTCAGTTGC 59.966 55.000 0.00 0.00 0.00 4.17
36 37 2.639327 CCGCCCCTTTTTGCCTCAG 61.639 63.158 0.00 0.00 0.00 3.35
39 40 1.984026 CATCCGCCCCTTTTTGCCT 60.984 57.895 0.00 0.00 0.00 4.75
43 44 0.687427 CCATCCATCCGCCCCTTTTT 60.687 55.000 0.00 0.00 0.00 1.94
64 65 4.408821 GCTCGGTGCCACCATCCA 62.409 66.667 15.45 0.00 38.47 3.41
65 66 3.628646 AAGCTCGGTGCCACCATCC 62.629 63.158 15.45 0.41 44.23 3.51
66 67 1.244019 AAAAGCTCGGTGCCACCATC 61.244 55.000 15.45 1.69 44.23 3.51
67 68 1.228552 AAAAGCTCGGTGCCACCAT 60.229 52.632 15.45 0.00 44.23 3.55
104 109 1.064952 GAGCAGAGCGAAGACTACTCC 59.935 57.143 0.00 0.00 0.00 3.85
105 110 1.064952 GGAGCAGAGCGAAGACTACTC 59.935 57.143 0.00 0.00 0.00 2.59
106 111 1.099689 GGAGCAGAGCGAAGACTACT 58.900 55.000 0.00 0.00 0.00 2.57
107 112 1.064952 GAGGAGCAGAGCGAAGACTAC 59.935 57.143 0.00 0.00 0.00 2.73
109 114 1.319614 GGAGGAGCAGAGCGAAGACT 61.320 60.000 0.00 0.00 0.00 3.24
110 115 1.140804 GGAGGAGCAGAGCGAAGAC 59.859 63.158 0.00 0.00 0.00 3.01
113 118 1.000270 AGAGGAGGAGCAGAGCGAA 60.000 57.895 0.00 0.00 0.00 4.70
114 119 1.453015 GAGAGGAGGAGCAGAGCGA 60.453 63.158 0.00 0.00 0.00 4.93
126 161 3.615811 AGCTGGTGGGGGAGAGGA 61.616 66.667 0.00 0.00 0.00 3.71
129 164 2.039624 GAGAGCTGGTGGGGGAGA 59.960 66.667 0.00 0.00 0.00 3.71
133 180 4.767255 GCACGAGAGCTGGTGGGG 62.767 72.222 13.31 0.00 39.30 4.96
137 184 4.427661 GCGAGCACGAGAGCTGGT 62.428 66.667 8.01 0.00 46.75 4.00
194 248 2.202570 CGCTCCATTGCTTGCTGC 60.203 61.111 0.00 0.00 43.25 5.25
255 309 4.890306 GGAGGGAGGGAGGGAGCC 62.890 77.778 0.00 0.00 0.00 4.70
256 310 4.890306 GGGAGGGAGGGAGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
257 311 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
265 319 4.179599 GGGGAGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
332 386 0.772124 AGACCAAGAAAGGGCCAGGA 60.772 55.000 6.18 0.00 37.41 3.86
335 389 0.555769 AACAGACCAAGAAAGGGCCA 59.444 50.000 6.18 0.00 37.41 5.36
349 403 1.228894 AGAGGAGGCGGTCAACAGA 60.229 57.895 0.00 0.00 0.00 3.41
350 404 1.216710 GAGAGGAGGCGGTCAACAG 59.783 63.158 0.00 0.00 0.00 3.16
360 414 3.299190 GATCCGGGCGAGAGGAGG 61.299 72.222 0.00 0.00 40.26 4.30
362 416 2.203365 GAGATCCGGGCGAGAGGA 60.203 66.667 0.00 0.00 41.30 3.71
447 501 4.093952 CACCGCCGAAAGCAGCAG 62.094 66.667 0.00 0.00 44.04 4.24
453 507 2.596338 AAACCCCACCGCCGAAAG 60.596 61.111 0.00 0.00 0.00 2.62
454 508 2.595172 GAAACCCCACCGCCGAAA 60.595 61.111 0.00 0.00 0.00 3.46
460 518 0.537371 AAGAGCAAGAAACCCCACCG 60.537 55.000 0.00 0.00 0.00 4.94
487 545 2.121506 AGACCCTGCCCCCAAGAA 60.122 61.111 0.00 0.00 0.00 2.52
555 618 1.658686 AACGGCCAAAAGAACGCACA 61.659 50.000 2.24 0.00 0.00 4.57
557 620 0.526524 CAAACGGCCAAAAGAACGCA 60.527 50.000 2.24 0.00 0.00 5.24
560 623 2.860971 GCTACCAAACGGCCAAAAGAAC 60.861 50.000 2.24 0.00 0.00 3.01
612 675 2.856628 CGGATCTCCATTCGCGGGA 61.857 63.158 6.13 4.00 35.14 5.14
669 732 3.092192 CTGTGAGCGAGCGCATTGG 62.092 63.158 17.68 0.00 44.88 3.16
710 773 1.522355 CGGTGATCGAAGCATGGCT 60.522 57.895 0.00 0.00 42.56 4.75
765 828 4.194720 CCGGTCGAGAAGGCGGAG 62.195 72.222 0.00 0.00 0.00 4.63
784 847 2.971598 ATTGGCGTCTCCCCTGTGG 61.972 63.158 0.00 0.00 0.00 4.17
785 848 1.746615 CATTGGCGTCTCCCCTGTG 60.747 63.158 0.00 0.00 0.00 3.66
786 849 2.671070 CATTGGCGTCTCCCCTGT 59.329 61.111 0.00 0.00 0.00 4.00
794 857 0.400213 TATCCATCCCCATTGGCGTC 59.600 55.000 0.00 0.00 34.06 5.19
818 881 0.296936 GCTATGATGATCATCGCGCG 59.703 55.000 26.76 26.76 36.16 6.86
819 882 1.323834 CTGCTATGATGATCATCGCGC 59.676 52.381 26.52 25.58 45.25 6.86
823 886 2.277969 CGGCCTGCTATGATGATCATC 58.722 52.381 25.91 25.91 38.26 2.92
824 887 1.627329 ACGGCCTGCTATGATGATCAT 59.373 47.619 13.10 13.10 40.72 2.45
848 911 0.658829 CGCGCTGCTGCTAGTACTAG 60.659 60.000 23.25 23.25 36.97 2.57
854 917 3.114616 AACACGCGCTGCTGCTAG 61.115 61.111 5.73 9.47 36.97 3.42
858 921 4.081030 CTCCAACACGCGCTGCTG 62.081 66.667 5.73 5.56 0.00 4.41
900 976 0.536233 CAACATCCCACGGAACACCA 60.536 55.000 0.00 0.00 34.34 4.17
937 1013 4.259356 CTGAGAAGATGAACCTGCATTCA 58.741 43.478 5.26 5.26 42.62 2.57
963 1042 1.548973 CCTGCGTCGTCACAGAACAC 61.549 60.000 0.00 0.00 35.90 3.32
977 1062 2.098298 CGGATCAAAACGCCTGCG 59.902 61.111 10.40 10.40 46.03 5.18
983 1068 4.178861 TCCTCGCGGATCAAAACG 57.821 55.556 6.13 0.00 33.30 3.60
1133 1218 3.882888 CAGCTCTAACTTGGAAACCACAA 59.117 43.478 0.00 0.00 30.78 3.33
1153 1238 7.281549 TGTTCTCATGGTTACAATCATCATCAG 59.718 37.037 0.00 0.00 0.00 2.90
1186 1317 6.296026 TGGTGTAAACAAAGCTCTTGAGTAT 58.704 36.000 13.35 2.59 0.00 2.12
1187 1318 5.676552 TGGTGTAAACAAAGCTCTTGAGTA 58.323 37.500 13.35 4.70 0.00 2.59
1188 1319 4.523083 TGGTGTAAACAAAGCTCTTGAGT 58.477 39.130 13.35 5.41 0.00 3.41
1189 1320 4.555511 GCTGGTGTAAACAAAGCTCTTGAG 60.556 45.833 13.35 0.00 35.87 3.02
1190 1321 3.315191 GCTGGTGTAAACAAAGCTCTTGA 59.685 43.478 13.35 0.00 35.87 3.02
1191 1322 3.550842 GGCTGGTGTAAACAAAGCTCTTG 60.551 47.826 14.99 6.98 37.72 3.02
1202 1337 0.854218 TTCCTTGGGGCTGGTGTAAA 59.146 50.000 0.00 0.00 0.00 2.01
1211 1346 1.005450 TCCAGTGTTATTCCTTGGGGC 59.995 52.381 0.00 0.00 0.00 5.80
1215 1368 2.673368 GACGCTCCAGTGTTATTCCTTG 59.327 50.000 0.00 0.00 39.12 3.61
1217 1370 1.207329 GGACGCTCCAGTGTTATTCCT 59.793 52.381 0.00 0.00 39.12 3.36
1219 1373 2.380084 TGGACGCTCCAGTGTTATTC 57.620 50.000 3.02 0.00 42.67 1.75
1229 1383 4.547532 CATACATAAGTACTGGACGCTCC 58.452 47.826 0.00 0.00 32.77 4.70
1231 1385 3.958798 ACCATACATAAGTACTGGACGCT 59.041 43.478 0.00 0.00 35.10 5.07
1235 1389 5.712752 AGCCTACCATACATAAGTACTGGA 58.287 41.667 0.00 0.00 35.10 3.86
1242 1396 7.534723 TGGTAACTAGCCTACCATACATAAG 57.465 40.000 16.73 0.00 43.11 1.73
1250 1404 5.129815 CCTATTTGTGGTAACTAGCCTACCA 59.870 44.000 16.73 16.73 45.23 3.25
1251 1405 5.364735 TCCTATTTGTGGTAACTAGCCTACC 59.635 44.000 12.71 12.71 39.51 3.18
1252 1406 6.097981 AGTCCTATTTGTGGTAACTAGCCTAC 59.902 42.308 0.00 0.00 37.61 3.18
1253 1407 6.200114 AGTCCTATTTGTGGTAACTAGCCTA 58.800 40.000 0.00 0.00 37.61 3.93
1263 1417 9.303116 CAGTATCTATCTAGTCCTATTTGTGGT 57.697 37.037 0.00 0.00 0.00 4.16
1347 1503 5.605488 TGGACCTCTGTAAAAAGGAAGTACT 59.395 40.000 0.00 0.00 36.46 2.73
1377 1534 8.615878 AAATTAGTACTATGTTCAACAGCACA 57.384 30.769 2.79 0.00 0.00 4.57
1406 1571 5.755375 ACATCAAGAATATGTGTAGCGAAGG 59.245 40.000 0.00 0.00 36.24 3.46
1411 1580 8.344831 TGCAATAACATCAAGAATATGTGTAGC 58.655 33.333 0.00 0.00 37.62 3.58
1465 1654 8.414778 TGGATTTAATGGTGTTTAAACTTTCGT 58.585 29.630 18.72 7.31 34.75 3.85
1492 1681 8.177980 GTTGATTCAACTTGGCAGATATTTTC 57.822 34.615 19.90 0.00 40.73 2.29
1612 1825 8.296713 GTGCCACATTTAAAAGTTCTGAGATTA 58.703 33.333 0.00 0.00 0.00 1.75
1626 1853 7.872881 TGTAAAGTAAATCGTGCCACATTTAA 58.127 30.769 11.44 0.00 0.00 1.52
1635 1862 8.269424 CAGATACTGATGTAAAGTAAATCGTGC 58.731 37.037 0.00 0.00 33.97 5.34
1639 1866 8.768955 CCAGCAGATACTGATGTAAAGTAAATC 58.231 37.037 14.26 0.00 45.08 2.17
1648 1875 2.224137 GCAGCCAGCAGATACTGATGTA 60.224 50.000 14.26 0.00 45.08 2.29
1689 1916 0.948678 GTCAAAAGTGGTTGGCGCTA 59.051 50.000 7.64 0.00 0.00 4.26
1694 1921 4.448537 TTGTGAAGTCAAAAGTGGTTGG 57.551 40.909 0.00 0.00 0.00 3.77
1709 1936 6.320926 TGAATGATTGAGAACTGGTTTGTGAA 59.679 34.615 0.00 0.00 0.00 3.18
1710 1937 5.827267 TGAATGATTGAGAACTGGTTTGTGA 59.173 36.000 0.00 0.00 0.00 3.58
1719 1946 8.693120 AATATGCTCATGAATGATTGAGAACT 57.307 30.769 0.00 0.00 41.53 3.01
1720 1947 9.395707 GAAATATGCTCATGAATGATTGAGAAC 57.604 33.333 0.00 0.00 41.53 3.01
1721 1948 9.350951 AGAAATATGCTCATGAATGATTGAGAA 57.649 29.630 0.00 0.00 41.53 2.87
1724 1951 9.788889 ACTAGAAATATGCTCATGAATGATTGA 57.211 29.630 0.00 0.00 36.02 2.57
1728 1955 9.842775 AGAAACTAGAAATATGCTCATGAATGA 57.157 29.630 0.00 0.00 35.16 2.57
1732 1960 8.489489 AGGAAGAAACTAGAAATATGCTCATGA 58.511 33.333 0.00 0.00 0.00 3.07
1736 1964 7.766278 TCACAGGAAGAAACTAGAAATATGCTC 59.234 37.037 0.00 0.00 0.00 4.26
1737 1965 7.624549 TCACAGGAAGAAACTAGAAATATGCT 58.375 34.615 0.00 0.00 0.00 3.79
1745 1973 6.879458 GCCTTTTATCACAGGAAGAAACTAGA 59.121 38.462 0.00 0.00 30.81 2.43
1763 1991 7.501225 GCCTACAGGATAAAACATAGCCTTTTA 59.499 37.037 0.00 0.00 37.39 1.52
1767 1995 4.660771 AGCCTACAGGATAAAACATAGCCT 59.339 41.667 0.00 0.00 37.39 4.58
1769 1997 7.878127 TCATAAGCCTACAGGATAAAACATAGC 59.122 37.037 0.00 0.00 37.39 2.97
1770 1998 9.209175 GTCATAAGCCTACAGGATAAAACATAG 57.791 37.037 0.00 0.00 37.39 2.23
1809 2037 4.836825 CCCTTGAAGTAGAATGAGCTCAA 58.163 43.478 22.50 0.00 0.00 3.02
1936 2164 3.374988 TCAGTTTGCCGCTATGAAATCTG 59.625 43.478 0.00 0.00 0.00 2.90
1938 2166 3.126858 TGTCAGTTTGCCGCTATGAAATC 59.873 43.478 0.00 0.00 0.00 2.17
1941 2169 2.177394 TGTCAGTTTGCCGCTATGAA 57.823 45.000 0.00 0.00 0.00 2.57
1948 2176 2.507339 AATTGGTTGTCAGTTTGCCG 57.493 45.000 0.00 0.00 0.00 5.69
2062 2290 4.700213 CGGAATGTAATAGGCCCATTAAGG 59.300 45.833 5.10 0.00 37.03 2.69
2175 2490 3.385755 AGCAATGAAACAAAAGTCCAGCT 59.614 39.130 0.00 0.00 0.00 4.24
2222 2537 2.948979 CCACAGAAACCTGTAAAGCACA 59.051 45.455 0.00 0.00 42.60 4.57
2386 2701 4.642437 TCGTTGCCAAATTATAGCATGGAA 59.358 37.500 0.00 0.00 36.20 3.53
2439 2758 8.947115 ACAAACAAGTTAGCAAATATCTAGACC 58.053 33.333 0.00 0.00 0.00 3.85
2444 2763 8.165239 TGTCACAAACAAGTTAGCAAATATCT 57.835 30.769 0.00 0.00 34.03 1.98
2497 2816 6.472686 AGAGTATGATGGAGTACCTGAAAC 57.527 41.667 0.00 0.00 37.04 2.78
2539 2858 3.338249 CTCCCCTGACAACATTGTGTAG 58.662 50.000 1.07 0.85 42.43 2.74
2671 2990 7.380536 ACAATGCATTTCAATCAACACTACAT 58.619 30.769 9.83 0.00 0.00 2.29
2686 3005 8.504812 ACCTTAAAACAAAGAACAATGCATTT 57.495 26.923 9.83 0.00 0.00 2.32
2702 3021 3.549423 GCGGTGTCAAGGAACCTTAAAAC 60.549 47.826 5.75 0.00 34.50 2.43
2729 3048 0.885879 TAGGCGCTCGACTTCTTCAA 59.114 50.000 7.64 0.00 34.01 2.69
2851 3170 8.820831 ACTGATCTGATCCCTTTATTATACTGG 58.179 37.037 14.71 0.00 0.00 4.00
2960 3281 5.722923 ACCCTACTAGTATAACAACCAAGCA 59.277 40.000 2.33 0.00 0.00 3.91
3022 3343 8.704668 TGAAAGAAGTAGACCAATGCTATGATA 58.295 33.333 0.00 0.00 0.00 2.15
3193 3514 7.467557 TCTGTTGTGAAATCAATTGAAAAGC 57.532 32.000 13.09 3.34 0.00 3.51
3351 3673 0.321298 TTCTGGTCCGCAAAGCCTAC 60.321 55.000 0.00 0.00 0.00 3.18
3358 3680 1.153066 TTGCACTTCTGGTCCGCAA 60.153 52.632 0.00 0.00 40.08 4.85
3378 3700 0.035439 CGGCAGGAACACCCAGTTAT 60.035 55.000 0.00 0.00 41.51 1.89
3456 3778 1.291272 GGCGTTGTACTTCCGGTCT 59.709 57.895 0.00 0.00 0.00 3.85
3610 3932 0.106318 GCCAGGAAATCCCAGCTCAT 60.106 55.000 0.00 0.00 37.41 2.90
3640 3963 6.763610 GGATTGGAATAGGAACTTCAGTACAG 59.236 42.308 0.00 0.00 41.75 2.74
3925 4254 7.497579 TGCATCGTGTGTGTAGGAATTTTATAT 59.502 33.333 0.00 0.00 0.00 0.86
3986 4315 5.809001 TGCTCCTAAGTTTGATGTTCAGAT 58.191 37.500 0.00 0.00 0.00 2.90
4016 4345 0.112412 GGTTGATTGTGTCCCCCAGT 59.888 55.000 0.00 0.00 0.00 4.00
4079 4430 6.887002 TGTTTGTCATGTAAATGCCCATACTA 59.113 34.615 0.00 0.00 0.00 1.82
4104 4455 6.127730 ACCTGTCTTTTCTTTTTCGTTCATGT 60.128 34.615 0.00 0.00 0.00 3.21
4146 4497 5.163364 CCTGTGCCTTATCTGACATACTCTT 60.163 44.000 0.00 0.00 0.00 2.85
4154 4505 1.208052 TGCTCCTGTGCCTTATCTGAC 59.792 52.381 0.00 0.00 0.00 3.51
4172 4523 1.028868 ATCCTGAAAGCGCCTCTTGC 61.029 55.000 2.29 0.00 34.67 4.01
4188 4539 5.508320 GGAGAGGAATCTCGACAAACTATCC 60.508 48.000 0.00 0.00 44.47 2.59
4245 4598 1.342819 GCTCCTCCTGAAGCATCGTAT 59.657 52.381 0.00 0.00 0.00 3.06


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.